| 1 | // this menu defines windows for two FastTree interfaces: nucleotide and protein |
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| 2 | // (depending on whether FASTTREE_NUC is defined or not) |
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| 3 | |
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| 4 | #ifdef FASTTREE_NUC |
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| 5 | # define SEQTYPE_NAME nucleotide |
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| 6 | # define SEQTYPE_SHRT NUC |
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| 7 | # define ST_FLAG -nt |
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| 8 | #else |
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| 9 | # define SEQTYPE_NAME protein |
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| 10 | # define SEQTYPE_SHRT PRO |
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| 11 | # define ST_FLAG |
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| 12 | #endif |
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| 13 | |
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| 14 | #define CLEANUP_INPUT \ |
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| 15 | arb_sed 's/#/>/' | \ |
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| 16 | arb_sed 's/%/>/' | \ |
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| 17 | arb_sed 's/"/>/' | \ |
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| 18 | arb_sed 's/@/>/' | \ |
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| 19 | arb_sed '/^[^>]/ y/./-/' |
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| 20 | |
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| 21 | #ifdef USE_OPENMP |
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| 22 | // depends on GUI |
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| 23 | # define FASTTREE_BINARY $ARBHOME/bin/$FASTTREE |
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| 24 | #else |
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| 25 | # define FASTTREE_BINARY $ARBHOME/bin/FastTree |
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| 26 | #endif |
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| 27 | |
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| 28 | #define FASTTREE_CODE \ |
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| 29 | (GOTO_LOCAL_DIR; \ |
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| 30 | <TmpInputFile CLEANUP_INPUT >fasttree_in; \ |
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| 31 | RUN_IN_WINDOW(( (FASTTREE_BINARY $NJMODE $NJ_OPT $MLMODEL -cat '$CAT' $SUPPORT ST_FLAG fasttree_in > fasttree_out || STOP_ON_FAILURE($FASTTREE)) && \ |
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| 32 | $DISPLAY_FUNC));)& |
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| 33 | |
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| 34 | item:FastTree2 (SEQTYPE_NAME) |
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| 35 | #ifdef FASTTREE_NUC |
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| 36 | itemmeta:F |
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| 37 | seqtype:N |
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| 38 | #else |
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| 39 | itemmeta:p |
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| 40 | seqtype:A |
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| 41 | #endif |
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| 42 | itemmethod: FASTTREE_CODE |
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| 43 | itemhelp: fasttree.help |
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| 44 | |
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| 45 | arg:DISPLAY_FUNC |
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| 46 | argtype:choice_menu |
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| 47 | arglabel:What to do with the tree? |
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| 48 | argchoice:Load into ARB ('tree_fasttree_//'):$ARBHOME/bin/arb_read_tree tree_fasttree_$$ fasttree_out "PRG=$FASTTREE$NJMODE FILTER=$FILTER MODEL=!$MLMODEL STYPE=SEQTYPE_SHRT" |
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| 49 | argchoice:Treetool:treetool fasttree_out |
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| 50 | |
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| 51 | #ifdef USE_OPENMP |
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| 52 | arg:FASTTREE |
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| 53 | argtype:choice_menu |
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| 54 | arglabel:Use multiprocessor? |
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| 55 | argchoice:No:FastTree |
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| 56 | argchoice:Yes:FastTreeMP |
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| 57 | #endif |
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| 58 | |
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| 59 | arg:NJMODE |
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| 60 | argtype:choice_menu |
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| 61 | arglabel:Neighbor joining phase |
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| 62 | argchoice:default: |
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| 63 | argchoice:fastest (recommended >50k species):-fastest |
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| 64 | argchoice:slow (really):-slow |
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| 65 | |
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| 66 | arg:NJ_OPT |
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| 67 | argtype:choice_menu |
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| 68 | arglabel:Weighted neighbor joining? |
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| 69 | argchoice:No: |
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| 70 | argchoice:Yes, as in BIONJ:-bionj |
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| 71 | |
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| 72 | arg:MLMODEL |
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| 73 | argtype:choice_menu |
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| 74 | arglabel:ML Model |
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| 75 | #ifdef FASTTREE_NUC |
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| 76 | argchoice:Jukes-Cantor: |
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| 77 | argchoice:GTR:-gtr |
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| 78 | #else |
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| 79 | argchoice:JTT: |
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| 80 | argchoice:WAG:-wag |
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| 81 | argchoice:LG:-lg |
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| 82 | #endif |
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| 83 | |
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| 84 | arg:CAT |
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| 85 | argtype:text |
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| 86 | arglabel:Number of rate categories\n(Range [1..n]; default: 20) |
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| 87 | argtext:20 |
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| 88 | |
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| 89 | arg:SUPPORT |
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| 90 | argtype:choice_menu |
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| 91 | arglabel:Support values |
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| 92 | argchoice:1000xresample + Shimodaira Hasegawa test: |
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| 93 | argchoice:Minimum-evolution bootstrap:-nome |
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| 94 | argchoice:None:-nosupport |
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| 95 | |
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| 96 | in:TmpInputFile |
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| 97 | informat:flat |
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| 98 | insave: |
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